Pathway enrichment analysis fGSEA
Low PTGS2 is the reference. When PTGS2 is high, pathways shown below are up- or down- regulated
fgsea_res <- fgsea_analysis(DE_res)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
fgp <- fgsea_plot(fgsea_res$res_hm, pathways_title='Hallmark', condition_name='PTGS2 low vs high')

kable(fgp)
| HALLMARK_TNFA_SIGNALING_VIA_NFKB |
0.0029586 |
0.0070442 |
0.6718790 |
3.434948 |
0 |
195 |
up |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
0.0028986 |
0.0070442 |
0.6070484 |
3.085146 |
0 |
189 |
up |
| HALLMARK_INFLAMMATORY_RESPONSE |
0.0029070 |
0.0070442 |
0.5254339 |
2.683342 |
0 |
193 |
up |
| HALLMARK_UV_RESPONSE_DN |
0.0027322 |
0.0070442 |
0.4620131 |
2.253674 |
0 |
136 |
up |
| HALLMARK_TGF_BETA_SIGNALING |
0.0024450 |
0.0070442 |
0.5363940 |
2.174837 |
0 |
54 |
up |
| HALLMARK_ANDROGEN_RESPONSE |
0.0025381 |
0.0070442 |
0.4704808 |
2.170916 |
0 |
96 |
up |
| HALLMARK_KRAS_SIGNALING_UP |
0.0029240 |
0.0070442 |
0.4210727 |
2.143357 |
0 |
190 |
up |
| HALLMARK_IL6_JAK_STAT3_SIGNALING |
0.0024450 |
0.0070442 |
0.4581458 |
2.060534 |
0 |
82 |
up |
| HALLMARK_APOPTOSIS |
0.0028490 |
0.0070442 |
0.4034059 |
1.993316 |
0 |
155 |
up |
| HALLMARK_ANGIOGENESIS |
0.0023641 |
0.0070442 |
0.5333233 |
1.966040 |
0 |
35 |
up |
| HALLMARK_IL2_STAT5_SIGNALING |
0.0029240 |
0.0070442 |
0.3818565 |
1.943737 |
0 |
190 |
up |
| HALLMARK_PROTEIN_SECRETION |
0.0024876 |
0.0070442 |
0.4154849 |
1.893443 |
0 |
89 |
up |
| HALLMARK_FATTY_ACID_METABOLISM |
0.0015432 |
0.0070442 |
-0.3946258 |
-1.830420 |
0 |
147 |
down |
| HALLMARK_XENOBIOTIC_METABOLISM |
0.0015198 |
0.0070442 |
-0.3755563 |
-1.801707 |
0 |
188 |
down |
| HALLMARK_HYPOXIA |
0.0027701 |
0.0070442 |
0.3520276 |
1.784744 |
0 |
180 |
up |
| HALLMARK_KRAS_SIGNALING_DN |
0.0015625 |
0.0070442 |
-0.3736344 |
-1.775946 |
0 |
179 |
down |
| HALLMARK_ALLOGRAFT_REJECTION |
0.0028818 |
0.0070442 |
0.3329580 |
1.693405 |
0 |
187 |
up |
| HALLMARK_GLYCOLYSIS |
0.0015198 |
0.0070442 |
-0.3449329 |
-1.654794 |
0 |
188 |
down |
| HALLMARK_COMPLEMENT |
0.0029070 |
0.0070442 |
0.3115283 |
1.590945 |
0 |
193 |
up |
| HALLMARK_MYC_TARGETS_V1 |
0.0028986 |
0.0070442 |
0.3121833 |
1.586581 |
0 |
189 |
up |
| HALLMARK_COAGULATION |
0.0027322 |
0.0070442 |
0.3205127 |
1.547631 |
0 |
127 |
up |
| HALLMARK_INTERFERON_ALPHA_RESPONSE |
0.0032949 |
0.0074884 |
-0.3704954 |
-1.591107 |
1 |
93 |
down |
| HALLMARK_INTERFERON_GAMMA_RESPONSE |
0.0057971 |
0.0126024 |
0.2858225 |
1.463917 |
1 |
194 |
up |
| HALLMARK_E2F_TARGETS |
0.0060698 |
0.0126454 |
-0.3057234 |
-1.466908 |
3 |
191 |
down |
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY |
0.0068376 |
0.0136752 |
-0.4506941 |
-1.682955 |
3 |
46 |
down |
| HALLMARK_CHOLESTEROL_HOMEOSTASIS |
0.0096154 |
0.0184911 |
0.3778151 |
1.622887 |
3 |
69 |
up |
fgp <- fgsea_plot(fgsea_res$res_c1, pathways_title='C1 positional genes', condition_name='PTGS2 low vs high')

kable(fgp)
| chr14q22 |
0.0024450 |
0.0089866 |
0.6480918 |
2.765761 |
0 |
62 |
up |
| chr17q25 |
0.0014925 |
0.0089866 |
-0.5605161 |
-2.703600 |
0 |
202 |
down |
| chr14q11 |
0.0014793 |
0.0089866 |
-0.5576148 |
-2.676253 |
0 |
196 |
down |
| chr2q33 |
0.0025907 |
0.0089866 |
0.5664097 |
2.666090 |
0 |
103 |
up |
| chr3q12 |
0.0023202 |
0.0089866 |
0.7217473 |
2.632674 |
0 |
30 |
up |
| chr5q22 |
0.0023364 |
0.0089866 |
0.6585974 |
2.544725 |
0 |
38 |
up |
| chr16p13 |
0.0014881 |
0.0089866 |
-0.5038103 |
-2.504243 |
0 |
272 |
down |
| chr5q11 |
0.0023529 |
0.0089866 |
0.6180480 |
2.471369 |
0 |
45 |
up |
| chr15q21 |
0.0026042 |
0.0089866 |
0.5242948 |
2.464045 |
0 |
102 |
up |
| chr16p11 |
0.0015924 |
0.0089866 |
-0.5485333 |
-2.450083 |
0 |
120 |
down |
| chr5p13 |
0.0025253 |
0.0089866 |
0.5180763 |
2.325249 |
0 |
84 |
up |
| chr8q24 |
0.0014970 |
0.0089866 |
-0.4854562 |
-2.313309 |
0 |
185 |
down |
| chr1p36 |
0.0013774 |
0.0089866 |
-0.4452136 |
-2.308809 |
0 |
395 |
down |
| chr13q22 |
0.0022936 |
0.0089866 |
0.6562163 |
2.294614 |
0 |
26 |
up |
| chr13q32 |
0.0024570 |
0.0089866 |
0.5285869 |
2.287202 |
0 |
67 |
up |
| chr9q33 |
0.0025974 |
0.0089866 |
0.4853644 |
2.284606 |
0 |
104 |
up |
| chr11q13 |
0.0014577 |
0.0089866 |
-0.4526367 |
-2.270298 |
0 |
290 |
down |
| chr2q31 |
0.0026110 |
0.0089866 |
0.4906042 |
2.261162 |
0 |
94 |
up |
| chr2p16 |
0.0023923 |
0.0089866 |
0.5483907 |
2.247815 |
0 |
51 |
up |
| chr2q32 |
0.0023981 |
0.0089866 |
0.5184409 |
2.228915 |
0 |
63 |
up |
| chr1q44 |
0.0024390 |
0.0089866 |
0.5490340 |
2.215533 |
0 |
48 |
up |
| chr8p23 |
0.0025063 |
0.0089866 |
0.4896963 |
2.198111 |
0 |
83 |
up |
| chr8p22 |
0.0022624 |
0.0089866 |
0.6335003 |
2.190745 |
0 |
25 |
up |
| chr7p11 |
0.0018315 |
0.0089866 |
-0.7038405 |
-2.171840 |
0 |
17 |
down |
| chr13q13 |
0.0023585 |
0.0089866 |
0.5372955 |
2.156761 |
0 |
46 |
up |
| chr12q21 |
0.0024213 |
0.0089866 |
0.4972314 |
2.154743 |
0 |
66 |
up |
| chr18p11 |
0.0025907 |
0.0089866 |
0.4664890 |
2.149495 |
0 |
93 |
up |
| chr11q14 |
0.0025126 |
0.0089866 |
0.4835247 |
2.130963 |
0 |
76 |
up |
| chr3p14 |
0.0025063 |
0.0089866 |
0.4744171 |
2.129527 |
0 |
83 |
up |
| chr13q33 |
0.0023202 |
0.0089866 |
0.5604843 |
2.127107 |
0 |
35 |
up |
fgp <- fgsea_plot(fgsea_res$res_c2, pathways_title='C2 curated genes', condition_name='PTGS2 low vs high')

kable(fgp)
| PHONG_TNF_TARGETS_UP |
0.0023753 |
0.0191175 |
0.7491497 |
3.178509 |
0 |
62 |
up |
| ANASTASSIOU_MULTICANCER_INVASIVENESS_SIGNATURE |
0.0023753 |
0.0191175 |
0.7340077 |
3.114265 |
0 |
62 |
up |
| CHEN_HOXA5_TARGETS_9HR_UP |
0.0029326 |
0.0191175 |
0.5944775 |
3.074291 |
0 |
211 |
up |
| ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF |
0.0030030 |
0.0191175 |
0.5855923 |
3.038171 |
0 |
219 |
up |
| PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN |
0.0025641 |
0.0191175 |
0.6237117 |
3.024216 |
0 |
128 |
up |
| BROCKE_APOPTOSIS_REVERSED_BY_IL6 |
0.0026596 |
0.0191175 |
0.6128985 |
2.992494 |
0 |
140 |
up |
| KEGG_RIBOSOME |
0.0024096 |
0.0191175 |
0.6687799 |
2.988530 |
0 |
81 |
up |
| TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP |
0.0024213 |
0.0191175 |
0.6959614 |
2.972521 |
0 |
66 |
up |
| UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN |
0.0024213 |
0.0191175 |
0.8018658 |
2.971768 |
0 |
34 |
up |
| PECE_MAMMARY_STEM_CELL_DN |
0.0025707 |
0.0191175 |
0.6026885 |
2.937909 |
0 |
132 |
up |
| REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY |
0.0024631 |
0.0191175 |
0.6396325 |
2.926438 |
0 |
94 |
up |
| REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE |
0.0024570 |
0.0191175 |
0.6205736 |
2.898645 |
0 |
104 |
up |
| REACTOME_EUKARYOTIC_TRANSLATION_ELONGATION |
0.0023810 |
0.0191175 |
0.6409805 |
2.895107 |
0 |
86 |
up |
| LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN |
0.0025575 |
0.0191175 |
0.5957315 |
2.894720 |
0 |
129 |
up |
| WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN |
0.0028571 |
0.0191175 |
0.5684874 |
2.894282 |
0 |
184 |
up |
| REACTOME_EUKARYOTIC_TRANSLATION_INITIATION |
0.0025126 |
0.0191175 |
0.6114179 |
2.885597 |
0 |
112 |
up |
| VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP |
0.0027855 |
0.0191175 |
0.5716292 |
2.852762 |
0 |
161 |
up |
| DAUER_STAT3_TARGETS_UP |
0.0023202 |
0.0191175 |
0.7096314 |
2.823669 |
0 |
46 |
up |
| NIKOLSKY_BREAST_CANCER_16P13_AMPLICON |
0.0016920 |
0.0191175 |
-0.6373712 |
-2.817941 |
0 |
105 |
down |
| AMIT_SERUM_RESPONSE_60_MCF10A |
0.0023202 |
0.0191175 |
0.6770909 |
2.817641 |
0 |
55 |
up |
| NAGASHIMA_NRG1_SIGNALING_UP |
0.0028490 |
0.0191175 |
0.5604463 |
2.800306 |
0 |
167 |
up |
| REACTOME_NONSENSE_MEDIATED_DECAY_NMD |
0.0024096 |
0.0191175 |
0.5907164 |
2.793886 |
0 |
108 |
up |
| ZHENG_FOXP3_TARGETS_IN_THYMUS_UP |
0.0028736 |
0.0191175 |
0.5448709 |
2.782158 |
0 |
189 |
up |
| IKEDA_MIR30_TARGETS_UP |
0.0025000 |
0.0191175 |
0.5828889 |
2.759508 |
0 |
113 |
up |
| SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_UP |
0.0023866 |
0.0191175 |
0.6159585 |
2.759291 |
0 |
80 |
up |
| ONDER_CDH1_TARGETS_1_DN |
0.0027174 |
0.0191175 |
0.5501922 |
2.755134 |
0 |
159 |
up |
| GROSS_HYPOXIA_VIA_ELK3_DN |
0.0026178 |
0.0191175 |
0.5572989 |
2.751890 |
0 |
145 |
up |
| FALVELLA_SMOKERS_WITH_LUNG_CANCER |
0.0023641 |
0.0191175 |
0.6189870 |
2.743006 |
0 |
75 |
up |
| FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_UP |
0.0022883 |
0.0191175 |
0.6804240 |
2.738318 |
0 |
49 |
up |
| CROONQUIST_STROMAL_STIMULATION_UP |
0.0022936 |
0.0191175 |
0.6569458 |
2.722766 |
0 |
54 |
up |
fgp <- fgsea_plot(fgsea_res$res_c3, pathways_title='C3 regulatory target genes', condition_name='PTGS2 low vs high')

kable(fgp)
| MIR3973 |
0.0029326 |
0.0092382 |
0.5470727 |
2.904792 |
0 |
244 |
up |
| MIR3617_5P |
0.0029412 |
0.0092382 |
0.5445195 |
2.887844 |
0 |
240 |
up |
| MIR641 |
0.0028902 |
0.0092382 |
0.5410508 |
2.877904 |
0 |
239 |
up |
| MIR576_5P |
0.0031646 |
0.0092382 |
0.5231541 |
2.863549 |
0 |
315 |
up |
| MIR410_3P |
0.0031250 |
0.0092382 |
0.5177129 |
2.818520 |
0 |
308 |
up |
| MIR4263 |
0.0028902 |
0.0092382 |
0.5282944 |
2.810051 |
0 |
239 |
up |
| MIR1252_3P |
0.0031646 |
0.0092382 |
0.5184203 |
2.793553 |
0 |
281 |
up |
| MIR32_3P |
0.0031348 |
0.0092382 |
0.5115229 |
2.788314 |
0 |
310 |
up |
| MIR7844_5P |
0.0028902 |
0.0092382 |
0.5715168 |
2.787608 |
0 |
141 |
up |
| MIR145_5P |
0.0031447 |
0.0092382 |
0.5154118 |
2.786194 |
0 |
287 |
up |
| MIR195_3P |
0.0029155 |
0.0092382 |
0.5332156 |
2.775448 |
0 |
214 |
up |
| CTTGTAT_MIR381 |
0.0028653 |
0.0092382 |
0.5421413 |
2.774851 |
0 |
187 |
up |
| MIR5195_3P |
0.0031746 |
0.0092382 |
0.5138148 |
2.770305 |
0 |
292 |
up |
| MIR16_2_3P |
0.0029070 |
0.0092382 |
0.5286843 |
2.750729 |
0 |
213 |
up |
| TAATGTG_MIR323 |
0.0028902 |
0.0092382 |
0.5567339 |
2.749844 |
0 |
152 |
up |
| ACTGAAA_MIR30A3P_MIR30E3P |
0.0028736 |
0.0092382 |
0.5345510 |
2.736554 |
0 |
190 |
up |
| ATGTTAA_MIR302C |
0.0029412 |
0.0092382 |
0.5165642 |
2.728647 |
0 |
231 |
up |
| MIR888_5P |
0.0029155 |
0.0092382 |
0.5198984 |
2.727298 |
0 |
222 |
up |
| MIR372_5P |
0.0030120 |
0.0092382 |
0.5179592 |
2.725813 |
0 |
230 |
up |
| ATTACAT_MIR3803P |
0.0027778 |
0.0092382 |
0.5935977 |
2.725732 |
0 |
96 |
up |
| MIR4789_3P |
0.0031646 |
0.0092382 |
0.4978131 |
2.725435 |
0 |
318 |
up |
| MIR518A_5P_MIR527 |
0.0029586 |
0.0092382 |
0.5061683 |
2.687815 |
0 |
242 |
up |
| MIR545_5P |
0.0031949 |
0.0092382 |
0.4958886 |
2.681790 |
0 |
296 |
up |
| MIR548AV_5P_MIR548K |
0.0031847 |
0.0092382 |
0.4965367 |
2.676839 |
0 |
282 |
up |
| MIR34C_3P |
0.0025063 |
0.0092382 |
0.6273882 |
2.673880 |
0 |
62 |
up |
| MIR8054 |
0.0031847 |
0.0092382 |
0.4937170 |
2.661637 |
0 |
282 |
up |
| MIR4760_5P |
0.0028169 |
0.0092382 |
0.5190253 |
2.641164 |
0 |
179 |
up |
| MIR7853_5P |
0.0029851 |
0.0092382 |
0.5118496 |
2.638307 |
0 |
206 |
up |
| CATTTCA_MIR203 |
0.0031546 |
0.0092382 |
0.4897187 |
2.630626 |
0 |
272 |
up |
| MIR586 |
0.0029851 |
0.0092382 |
0.4926144 |
2.627582 |
0 |
258 |
up |
fgp <- fgsea_plot(fgsea_res$res_c4, pathways_title='C4 cancer', condition_name='PTGS2 low vs high')

kable(fgp)
| GNF2_PTX3 |
0.0025641 |
0.0175245 |
0.7760591 |
2.946426 |
0 |
35 |
up |
| GNF2_MMP1 |
0.0025510 |
0.0175245 |
0.7942854 |
2.928803 |
0 |
31 |
up |
| GNF2_ST13 |
0.0026385 |
0.0175245 |
0.6885203 |
2.896663 |
0 |
58 |
up |
| GNF2_DAP3 |
0.0027933 |
0.0175245 |
0.5988357 |
2.822404 |
0 |
110 |
up |
| GNF2_EIF3S6 |
0.0027933 |
0.0175245 |
0.5983728 |
2.820222 |
0 |
110 |
up |
| GNF2_RBBP6 |
0.0026525 |
0.0175245 |
0.6455645 |
2.816427 |
0 |
68 |
up |
| GNF2_TPT1 |
0.0025641 |
0.0175245 |
0.7123200 |
2.712772 |
0 |
36 |
up |
| MORF_TPT1 |
0.0027701 |
0.0175245 |
0.5823326 |
2.676855 |
0 |
92 |
up |
| GCM_TPT1 |
0.0026596 |
0.0175245 |
0.6309535 |
2.671192 |
0 |
59 |
up |
| MODULE_239 |
0.0027701 |
0.0175245 |
0.5363332 |
2.538283 |
0 |
111 |
up |
| MORF_JUND |
0.0025773 |
0.0175245 |
0.5938818 |
2.509412 |
0 |
55 |
up |
| GCM_CSNK1A1 |
0.0025840 |
0.0175245 |
0.6637386 |
2.497259 |
0 |
34 |
up |
| GNF2_CDC20 |
0.0016129 |
0.0175245 |
-0.6465991 |
-2.493244 |
0 |
53 |
down |
| GNF2_PPP6C |
0.0025641 |
0.0175245 |
0.6556029 |
2.489096 |
0 |
35 |
up |
| GNF2_FBL |
0.0029326 |
0.0175245 |
0.5094511 |
2.478444 |
0 |
133 |
up |
| GNF2_CCNB2 |
0.0016234 |
0.0175245 |
-0.6396793 |
-2.469800 |
0 |
54 |
down |
| MODULE_332 |
0.0024570 |
0.0175245 |
0.6176494 |
2.467339 |
0 |
44 |
up |
| GNF2_TST |
0.0015773 |
0.0175245 |
-0.5710539 |
-2.464096 |
0 |
95 |
down |
| GNF2_CDH11 |
0.0025575 |
0.0175245 |
0.7201195 |
2.462748 |
0 |
25 |
up |
| MORF_ACTG1 |
0.0029326 |
0.0175245 |
0.5093717 |
2.455888 |
0 |
127 |
up |
| GNF2_PCNA |
0.0016026 |
0.0175245 |
-0.6142481 |
-2.454073 |
0 |
65 |
down |
| GCM_RAB10 |
0.0029155 |
0.0175245 |
0.4838825 |
2.445160 |
0 |
165 |
up |
| GNF2_GSTM1 |
0.0015649 |
0.0175245 |
-0.5600549 |
-2.443284 |
0 |
101 |
down |
| GNF2_CCNA2 |
0.0016026 |
0.0175245 |
-0.6099155 |
-2.436763 |
0 |
65 |
down |
| GNF2_ESPL1 |
0.0016340 |
0.0175245 |
-0.6894501 |
-2.422100 |
0 |
35 |
down |
| GCM_ZNF198 |
0.0027701 |
0.0175245 |
0.5077790 |
2.403145 |
0 |
111 |
up |
| MODULE_29 |
0.0025510 |
0.0175245 |
0.6916385 |
2.399001 |
0 |
26 |
up |
| GCM_NPM1 |
0.0028169 |
0.0175245 |
0.5074841 |
2.382291 |
0 |
104 |
up |
| GCM_HBP1 |
0.0026316 |
0.0175245 |
0.5580037 |
2.381155 |
0 |
61 |
up |
| MORF_NPM1 |
0.0029240 |
0.0175245 |
0.4752601 |
2.364476 |
0 |
149 |
up |
fgp <- fgsea_plot(fgsea_res$res_c5, pathways_title='C5 GO genes', condition_name='PTGS2 low vs high')

kable(fgp)
fgp <- fgsea_plot(fgsea_res$res_c6, pathways_title='C6 oncogenic', condition_name='PTGS2 low vs high')

kable(fgp)
| PIGF_UP.V1_UP |
0.0029762 |
0.0114379 |
0.5753524 |
2.988685 |
0 |
181 |
up |
| EGFR_UP.V1_UP |
0.0029940 |
0.0114379 |
0.5494265 |
2.849799 |
0 |
180 |
up |
| VEGF_A_UP.V1_DN |
0.0029499 |
0.0114379 |
0.5179745 |
2.698541 |
0 |
184 |
up |
| CSR_EARLY_UP.V1_UP |
0.0028090 |
0.0114379 |
0.5059503 |
2.530878 |
0 |
139 |
up |
| HOXA9_DN.V1_UP |
0.0029940 |
0.0114379 |
0.4711044 |
2.413539 |
0 |
170 |
up |
| HINATA_NFKB_IMMU_INF |
0.0022883 |
0.0114379 |
0.8305516 |
2.404089 |
0 |
14 |
up |
| BMI1_DN_MEL18_DN.V1_UP |
0.0028090 |
0.0114379 |
0.4664368 |
2.312802 |
0 |
135 |
up |
| SIRNA_EIF4GI_DN |
0.0025907 |
0.0114379 |
0.4922075 |
2.242667 |
0 |
88 |
up |
| ATF2_UP.V1_DN |
0.0030211 |
0.0114379 |
0.4173613 |
2.142560 |
0 |
171 |
up |
| PRC2_EED_UP.V1_DN |
0.0014815 |
0.0114379 |
-0.4511859 |
-2.135430 |
0 |
179 |
down |
| PDGF_UP.V1_UP |
0.0028986 |
0.0114379 |
0.4345148 |
2.131017 |
0 |
133 |
up |
| TGFB_UP.V1_UP |
0.0030675 |
0.0114379 |
0.4141101 |
2.128501 |
0 |
176 |
up |
| BCAT_BILD_ET_AL_DN |
0.0023753 |
0.0114379 |
0.5238755 |
2.089688 |
0 |
45 |
up |
| RPS14_DN.V1_UP |
0.0029326 |
0.0114379 |
0.4017856 |
2.088159 |
0 |
182 |
up |
| CAMP_UP.V1_DN |
0.0029851 |
0.0114379 |
0.4011555 |
2.086744 |
0 |
186 |
up |
| ERBB2_UP.V1_DN |
0.0029326 |
0.0114379 |
0.3924639 |
2.039712 |
0 |
182 |
up |
| E2F1_UP.V1_DN |
0.0030675 |
0.0114379 |
0.3929226 |
2.019599 |
0 |
176 |
up |
| KRAS.50_UP.V1_UP |
0.0023753 |
0.0114379 |
0.5052717 |
2.015479 |
0 |
45 |
up |
| SRC_UP.V1_UP |
0.0015361 |
0.0114379 |
-0.4361672 |
-2.008377 |
0 |
148 |
down |
| RAF_UP.V1_UP |
0.0030581 |
0.0114379 |
0.3845223 |
1.987339 |
0 |
179 |
up |
| LTE2_UP.V1_DN |
0.0029326 |
0.0114379 |
0.3775259 |
1.962077 |
0 |
182 |
up |
| KRAS.KIDNEY_UP.V1_UP |
0.0027701 |
0.0114379 |
0.3983047 |
1.959377 |
0 |
130 |
up |
| EIF4E_DN |
0.0025126 |
0.0114379 |
0.4228544 |
1.957938 |
0 |
94 |
up |
| BMI1_DN.V1_UP |
0.0028986 |
0.0114379 |
0.3974161 |
1.949072 |
0 |
133 |
up |
| RELA_DN.V1_UP |
0.0028329 |
0.0114379 |
0.3902186 |
1.918080 |
0 |
131 |
up |
| KRAS.300_UP.V1_UP |
0.0027701 |
0.0114379 |
0.3873041 |
1.905262 |
0 |
130 |
up |
| ATF2_S_UP.V1_DN |
0.0030211 |
0.0114379 |
0.3701727 |
1.899403 |
0 |
172 |
up |
| KRAS.DF.V1_UP |
0.0030864 |
0.0114379 |
0.3654774 |
1.885511 |
0 |
178 |
up |
| NFE2L2.V2 |
0.0013245 |
0.0114379 |
-0.3509105 |
-1.823915 |
0 |
395 |
down |
| KRAS.LUNG.BREAST_UP.V1_UP |
0.0027397 |
0.0114379 |
0.3728237 |
1.818569 |
0 |
124 |
up |
fgp <- fgsea_plot(fgsea_res$res_c7, pathways_title='C7 immunologic', condition_name='PTGS2 low vs high')

kable(fgp)
| GSE9988_LOW_LPS_VS_CTRL_TREATED_MONOCYTE_UP |
0.0028571 |
0.01013 |
0.6626050 |
3.353794 |
0 |
178 |
up |
| GSE9988_LOW_LPS_VS_VEHICLE_TREATED_MONOCYTE_UP |
0.0028490 |
0.01013 |
0.6476534 |
3.270482 |
0 |
175 |
up |
| GSE14769_UNSTIM_VS_80MIN_LPS_BMDM_DN |
0.0029499 |
0.01013 |
0.6270112 |
3.208241 |
0 |
191 |
up |
| GSE9988_LPS_VS_CTRL_TREATED_MONOCYTE_UP |
0.0028490 |
0.01013 |
0.6315690 |
3.189260 |
0 |
175 |
up |
| GSE14769_UNSTIM_VS_60MIN_LPS_BMDM_DN |
0.0029240 |
0.01013 |
0.6206065 |
3.187954 |
0 |
192 |
up |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_UP |
0.0028090 |
0.01013 |
0.6278268 |
3.176728 |
0 |
176 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_KO_4H_UP |
0.0027933 |
0.01013 |
0.6155783 |
3.142757 |
0 |
181 |
up |
| GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_DN |
0.0028329 |
0.01013 |
0.6165688 |
3.114530 |
0 |
172 |
up |
| GSE29617_CTRL_VS_DAY7_TIV_FLU_VACCINE_PBMC_2008_UP |
0.0028329 |
0.01013 |
0.6123084 |
3.112872 |
0 |
180 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_KO_2H_UP |
0.0028571 |
0.01013 |
0.6108320 |
3.094866 |
0 |
179 |
up |
| GSE21678_WT_VS_FOXO1_FOXO3_KO_TREG_UP |
0.0028490 |
0.01013 |
0.6032215 |
3.046112 |
0 |
175 |
up |
| GSE42021_TREG_PLN_VS_CD24INT_TREG_THYMUS_UP |
0.0028653 |
0.01013 |
0.5868058 |
3.033942 |
0 |
195 |
up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_CTRL_TREATED_MONOCYTES_UP |
0.0028249 |
0.01013 |
0.5888956 |
2.979970 |
0 |
177 |
up |
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_UP |
0.0028329 |
0.01013 |
0.5848084 |
2.973066 |
0 |
180 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_HET_2H_UP |
0.0028571 |
0.01013 |
0.5758679 |
2.917715 |
0 |
179 |
up |
| GSE27434_WT_VS_DNMT1_KO_TREG_DN |
0.0029586 |
0.01013 |
0.5675373 |
2.910922 |
0 |
193 |
up |
| GSE9988_ANTI_TREM1_VS_CTRL_TREATED_MONOCYTES_UP |
0.0028090 |
0.01013 |
0.5681529 |
2.904666 |
0 |
183 |
up |
| GSE12392_IFNAR_KO_VS_IFNB_KO_CD8_NEG_SPLEEN_DC_UP |
0.0028736 |
0.01013 |
0.5690880 |
2.903194 |
0 |
184 |
up |
| GSE30971_WBP7_HET_VS_KO_MACROPHAGE_2H_LPS_STIM_DN |
0.0029412 |
0.01013 |
0.5680119 |
2.902387 |
0 |
189 |
up |
| GSE29617_CTRL_VS_TIV_FLU_VACCINE_PBMC_2008_UP |
0.0028409 |
0.01013 |
0.5708043 |
2.879920 |
0 |
171 |
up |
| GSE14769_UNSTIM_VS_40MIN_LPS_BMDM_DN |
0.0029070 |
0.01013 |
0.5583699 |
2.877856 |
0 |
194 |
up |
| GSE9988_ANTI_TREM1_VS_VEHICLE_TREATED_MONOCYTES_UP |
0.0028090 |
0.01013 |
0.5663335 |
2.865580 |
0 |
176 |
up |
| GSE9988_ANTI_TREM1_VS_LOW_LPS_MONOCYTE_DN |
0.0028090 |
0.01013 |
0.5565787 |
2.845193 |
0 |
182 |
up |
| GSE14769_UNSTIM_VS_120MIN_LPS_BMDM_DN |
0.0028736 |
0.01013 |
0.5487134 |
2.835748 |
0 |
197 |
up |
| GSE2706_UNSTIM_VS_2H_LPS_DC_DN |
0.0028090 |
0.01013 |
0.5568357 |
2.817522 |
0 |
176 |
up |
| GSE45365_NK_CELL_VS_CD11B_DC_DN |
0.0029070 |
0.01013 |
0.5440801 |
2.804206 |
0 |
194 |
up |
| GSE9988_ANTI_TREM1_VS_LPS_MONOCYTE_DN |
0.0028090 |
0.01013 |
0.5473705 |
2.798121 |
0 |
182 |
up |
| GSE37605_FOXP3_FUSION_GFP_VS_IRES_GFP_TREG_C57BL6_DN |
0.0028409 |
0.01013 |
0.5543919 |
2.792489 |
0 |
166 |
up |
| GSE1791_CTRL_VS_NEUROMEDINU_IN_T_CELL_LINE_6H_UP |
0.0028653 |
0.01013 |
0.5434117 |
2.788647 |
0 |
187 |
up |
| GSE42021_TCONV_PLN_VS_TREG_PRECURSORS_THYMUS_DN |
0.0028490 |
0.01013 |
0.5330160 |
2.763932 |
0 |
196 |
up |
fgp <- fgsea_plot(fgsea_res$res_msg, pathways_title='All signatures', condition_name='PTGS2 low vs high')

kable(fgp)
| HALLMARK_TNFA_SIGNALING_VIA_NFKB |
0.0030864 |
0.0185283 |
0.6718790 |
3.469995 |
0 |
195 |
up |
| GSE9988_LOW_LPS_VS_CTRL_TREATED_MONOCYTE_UP |
0.0030395 |
0.0185283 |
0.6626050 |
3.383800 |
0 |
178 |
up |
| GSE9988_LOW_LPS_VS_VEHICLE_TREATED_MONOCYTE_UP |
0.0030303 |
0.0185283 |
0.6476534 |
3.295345 |
0 |
175 |
up |
| GSE14769_UNSTIM_VS_80MIN_LPS_BMDM_DN |
0.0030675 |
0.0185283 |
0.6270112 |
3.226162 |
0 |
191 |
up |
| PHONG_TNF_TARGETS_UP |
0.0025189 |
0.0185283 |
0.7491497 |
3.217832 |
0 |
62 |
up |
| GSE9988_LPS_VS_CTRL_TREATED_MONOCYTE_UP |
0.0030303 |
0.0185283 |
0.6315690 |
3.213505 |
0 |
175 |
up |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_UP |
0.0030120 |
0.0185283 |
0.6278268 |
3.191632 |
0 |
176 |
up |
| GSE14769_UNSTIM_VS_60MIN_LPS_BMDM_DN |
0.0031250 |
0.0185283 |
0.6206065 |
3.190041 |
0 |
192 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_KO_4H_UP |
0.0030488 |
0.0185283 |
0.6155783 |
3.154019 |
0 |
181 |
up |
| ANASTASSIOU_MULTICANCER_INVASIVENESS_SIGNATURE |
0.0025189 |
0.0185283 |
0.7340077 |
3.152793 |
0 |
62 |
up |
| GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_DN |
0.0029674 |
0.0185283 |
0.6165688 |
3.133817 |
0 |
172 |
up |
| GSE29617_CTRL_VS_DAY7_TIV_FLU_VACCINE_PBMC_2008_UP |
0.0030488 |
0.0185283 |
0.6123084 |
3.131190 |
0 |
180 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_KO_2H_UP |
0.0030581 |
0.0185283 |
0.6108320 |
3.118400 |
0 |
179 |
up |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
0.0031153 |
0.0185283 |
0.6070484 |
3.104894 |
0 |
189 |
up |
| CHEN_HOXA5_TARGETS_9HR_UP |
0.0031949 |
0.0185283 |
0.5944775 |
3.078689 |
0 |
211 |
up |
| GSE21678_WT_VS_FOXO1_FOXO3_KO_TREG_UP |
0.0030303 |
0.0185283 |
0.6032215 |
3.069269 |
0 |
175 |
up |
| ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF |
0.0031056 |
0.0185283 |
0.5855923 |
3.060070 |
0 |
219 |
up |
| GABRIELY_MIR21_TARGETS |
0.0032787 |
0.0185283 |
0.5621520 |
3.047059 |
0 |
271 |
up |
| STK33_NOMO_UP |
0.0032787 |
0.0185283 |
0.5656353 |
3.046990 |
0 |
267 |
up |
| PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN |
0.0027548 |
0.0185283 |
0.6237117 |
3.034484 |
0 |
128 |
up |
| GSE42021_TREG_PLN_VS_CD24INT_TREG_THYMUS_UP |
0.0030864 |
0.0185283 |
0.5868058 |
3.030625 |
0 |
195 |
up |
| MODULE_47 |
0.0030960 |
0.0185283 |
0.5783163 |
3.018859 |
0 |
214 |
up |
| UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN |
0.0023641 |
0.0185283 |
0.8018658 |
3.018412 |
0 |
34 |
up |
| BROCKE_APOPTOSIS_REVERSED_BY_IL6 |
0.0028490 |
0.0185283 |
0.6128985 |
3.014087 |
0 |
140 |
up |
| GO_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE |
0.0024938 |
0.0185283 |
0.6543159 |
3.014020 |
0 |
94 |
up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_CTRL_TREATED_MONOCYTES_UP |
0.0030303 |
0.0185283 |
0.5888956 |
2.999346 |
0 |
177 |
up |
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_UP |
0.0030488 |
0.0185283 |
0.5848084 |
2.990562 |
0 |
180 |
up |
| STK33_UP |
0.0033003 |
0.0185283 |
0.5542519 |
2.984593 |
0 |
263 |
up |
| KEGG_RIBOSOME |
0.0025253 |
0.0185283 |
0.6687799 |
2.976542 |
0 |
81 |
up |
| TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP |
0.0026596 |
0.0185283 |
0.6959614 |
2.969446 |
0 |
66 |
up |
y <- read.csv('/Users/senosam/Documents/Massion_lab/radiomics_summary/TMA36_CANARY_khushbu.csv')
vsd_mat <- t(ls_preprocessed$vsd_mat)
p_all <- ls_preprocessed$p_all
p_all <- cbind(p_all, 'SILA_S' = y$SILA_S[match(p_all$pt_ID, y$pt_ID)])
vsd_mat <- data.frame(cbind(vsd_mat, 'SILA_S'=p_all$SILA_S))
COX1 = "ENSG00000198804.2"
COX2 = "ENSG00000073756.7"
ggpubr::ggscatter(vsd_mat, x = "SILA_S", y = c(COX1, COX2),
add = "reg.line", conf.int = TRUE, combine = TRUE, scales='free',
cor.coef = TRUE, add.params = list(color = 'grey65'), expand = c(0, 0),
cor.coeff.args = list(method = "spearman"),
xlab = "SILA score", ylab = 'VST (gene expression)') +
ggpubr::font("xy.text", size = 10) +
ggpubr::font("xlab", size = 12, face = 'bold') +
ggpubr::font("ylab", size = 12, face = 'bold')
## `geom_smooth()` using formula 'y ~ x'
